Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryonic fibroblast
Cell type
MEF
Tissue
Embryonic Fibroblast
Lineage
primaryCells
Description
Mouse Embryonic Fibroblast

Attributes by original data submitter

Sample

source_name
connective tissue, mouse embryonic fibroblast
cell type
mouse embryonic fibroblast
strain
BALB/c
age
10.5 day old embryos
genotype
Actb +/+
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
50 ug total fragmented chromatin were mixed with 7 ug antibody overnight at 4 degree with rotation. The chromatin-antibody complex were then precipitated with protein A/G magnetic beads (Thermo Fisher Scientific). After washes with low salt wash buffer (20mM Tris, 2mM EDTA, 50mM NaCl, 0.01% SDS and 1% SDS), high salt wash buffer (same composition, 250 mM NaCl) and LiCL-wash buffer (10mM Tris, 1mM EDTA, 250 mM LiCl, 1% NP40 and 1% sodium deoxycholate), precipitated chromatin was eluted in 200µl of elution buffer (10µl 20% SDS, 20µl 1M NaHCO3 and 170µl dH2O). Reverse cross linking was done by adding 8 ul 5M NaCl and incubate at 65 deg overnight. 1 ul 10 mg/ml RNase A was added to the tube for 30 mins incubation at 37°C. Then 4µl 0.5M EDTA, 8µl 1M Tris-HCl and 1µl 20 mg/ml Proteinase K was added for 2h incubation at 42°C. The released DNA was purified using QIAquick PCR purification kit (Qiagen). Two biological replicates were prepared for library preparation using TruSeq Nano DNA Library Prep Kit (Illumina) according to the manufacturer's instructions

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
42596137
Reads aligned (%)
92.9
Duplicates removed (%)
33.9
Number of peaks
2737 (qval < 1E-05)

mm9

Number of total reads
42596137
Reads aligned (%)
92.6
Duplicates removed (%)
33.9
Number of peaks
2600 (qval < 1E-05)

Base call quality data from DBCLS SRA